Table I. Calculating the masses of positively charged fragment ions. [N] is the mass of the N-terminus (e.g., 1.0078 Da for unmodified peptides and 43.0184 Da for acetylated N-terminus). [C] is the mass of the C-terminus (e.g., 17.0027 Da for unmodified peptides and 16.0187 Da for amidated C-terminus). [M] is the sum of the amino acid residue masses (see Table II) that are contained within the fragment ion. CO is the combined mass of oxygen plus carbon atoms (27.9949 Da) and H is the mass of a proton (1.0078 Da). To calculate the m/z value of a fragment ion, add the mass of the protons to the neutral mass calculated from the table, and divide by the number of protons added.

Ion Type	Neutral MW of the fragment
a	[N] + [M] - CO - H
a.	[N] + [M] - CO
a-H2O	a – 18.0106
a-NH3	a – 17.0266
b	[N] + [M] - H
b-H2O	b – 18.0106
b-NH3	b – 17.0266
c	[N] + [M] + NH2
d	a – partial side chain
x	[C] + [M] + CO - H
y	[C] + [M] + H
y-H2O	y – 18.0106
y-NH3	y – 17.0266
z	[C] + [M] - NH
v	y - complete side chain
w	z - partial side chain